Ehrenberg was appointed professor of medicine at Berlin University in 1827. In 1829 he accompanied Humboldt through eastern Russia to the Chinese frontier. After his return he began to concentrate his studies on microscopic organisms, which then were not much studied.

These researches built up our knowledge of the microorganisms of certain geological formations, especially of the chalk, and of the marine and freshwater accumulations. Until Ehrenberg took up the study it was not known that considerable masses of rock were composed of minute forms of animals or plants. He also demonstrated that the phosphorescence of the sea was due to organisms.

After his death in 1876, his collections of microscopic organisms were deposited in the Humboldt Museum at the University of Berlin. The "Ehrenberg Collection" includes 40,000 microscope preparations, 5,000 raw samples, 3,000 pencil and ink drawings, and nearly 1,000 letters of correspondence. His collection of scorpions, and other arachnids from the Middle East, is also held in the Berlin Museum.